CHIMICA DELLE PROTEINE E PROTEOMICA

The aim of the course is to provide students with the most recent and updated basic knowledge in the field of protein chemistry and proteome analysis. Particularly, this knowledge will be useful to address the characterization of complex protein mixtures via proteomic approaches, involving the use of electrophoretic and chromatographic techniques, protein enzymatic digestion (in-gel and in solution), mass spectrometry analysis and, bioinformatics tools.

Furthermore, in reference to the so-called Dublin Descriptors, this course helps to acquire the following skills:

D1 - Knowledge and understanding: The students will have to demonstrate their basic knowledge related to the analytical methods used in proteomics.

D2 - Ability to apply knowledge: The student should be able to apply the acquired knowledge, in an appropriate and flexible way, for the characterization of complex protein mixtures.

D3 - Autonomy of judgment: The students will have to apply their knowledge, understanding and skills in proteomics. Particularly, the students should be able to develop an experimental project, also through the choice of the most appropriate analytical strategies.

D4 - Communication skills: The students must be able to communicate clearly with a correct property of language and terminological rigor their conclusions.

D5 - Learning skills: The students will have to develop learning skills that will enable them to continue studying in a self-directed or autonomous way.

Information for students with disabilities and/or Specific Learning Disabilities (SLD)

The students with disabilities and/or Specific Learning Disabilities (SLD) may contact the teacher to arrange a date and report any specific need they may have, and to plan any compensatory and/or dispensatory measures.

Classroom Lectures: 35 hours in classroom

Laboratory Training: 12 hours will be focused on the use of the mass spectrometer and bio-informatics softwares for the characterization of protein and peptide mixtures. 

The students should have basic knowledge of:

- protein chemistry

- liquid chromatography and electrophoresis

- mass spectrometry

Introduction. Review about the amino acids characteristics and properties, peptide bond and proteins. Post-translational modifications. From proteins to the proteome. Proteome Complexity and variability. Proteome characterization: the proteomics era. Proteins Expression and Functional Proteomics. Relationship between proteomics and the other omics sciences. Overview on the analytical techniques used in proteomics.

Mass spectrometry for peptides and proteins. Review of the basic concepts of mass spectrometry. ESI and MALDI ionization. Tandem Mass Spectrometry (MS/MS). Characterization of the peptide sequence by MS/MS. Characterization of the amino acid sequence of a protein by MS-based approaches. Interpretation of the MS/MS data: de novo sequencing.

Proteomics Strategies. Sample preparation: Proteins extraction from the sample. Top-down, middle-down and bottom-up proteomic approaches. Gel-based and gel-free approaches. Protein databases. Protein identification by mass spectrometry: Mascot and PEAKS software. Quantitative Proteomics: SILAC, ICAT and iTRAQ approaches; label-free approaches. Analysis of post-translational modifications. Examples and practical applications.

Outline of Bioinformatics applied to the study of protein sequences. Alignment methods of protein sequences. The Dot Matrix and the Substitution Matrices. Similarity search in databases by heuristic algorithms: FASTA and BLAST. Multiple sequence alignment: the ClustalW software.

Proteomica – T. Alberio; M. Fasano; P. Roncada; EDISES

Computational Methods for Mass Spectrometry Proteomics – I. Eidhammer; K. Flikka; L. Martens; S.O. Mikalsen; WILEY

Proteomics in Practice: A Laboratory Manual of Proteome Analysis – R. Westermeier;  T. Naven; WILEY

Oral examinations

link: http://www.dsc.unict.it/corsi/lm-54-org/esami

link: http://www.dsc.unict.it/docenti/vincenzo.cunsolo